Loci with P ≤ 10−7 in the conventional, intensive, or combined treatment groups using repeated A1C values (stage 2)
| Chromosome . | SNP . | Position . | Repeated A1C P value . | Mean A1C P value . | Mean A1C by genotype from repeated analysis . | A1 . | A2 . | Minor allele frequency . | Missing data* . | Hardy-Weinberg equilibrium . | Location of SNP to nearest gene . | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C homo (SE) . | Het (SE) . | R homo (SE) . | |||||||||||
| Conventional treatment group | |||||||||||||
| 9 | rs10810632 | 16,779,024 | 9.0 × 10−8 | 3.7 × 10−7 | 8.83 (0.05) | 9.50 (0.13) | 10.50 (0.63) | C | T | 0.08 | 1 | 0.70 | Intron 1 BNC2 |
| 9 | rs6475082 | 16,779,436 | 1.8 × 10−7 | 7.4 × 10−7 | 8.83 (0.05) | 9.48 (0.13) | 10.50 (0.63) | G | A | 0.08 | 1 | 0.71 | Intron 1 BNC2 |
| 9 | rs4961760 | 16,779,878 | 1.6 × 10−7 | 7.1 × 10−7 | 8.83 (0.05) | 9.48 (0.13) | 10.50 (0.63) | C | T | 0.08 | 0 | 0.71 | Intron 1 BNC2 |
| 9 | rs2254193 | 16,791,850 | 2.0 × 10−7 | 1.1 × 10−6 | 8.84 (0.05) | 9.57 (0.15) | 10.47 (0.70) | C | A | 0.07 | 8 | 0.67 | Intron 1 BNC2 |
| 10 | rs1358030 | 108,113,589 | 6.9 × 10−10 | 5.4 × 10−9 | 8.58 (0.07) | 9.12 (0.07) | 9.32 (0.13) | C | T | 0.36 | 2 | 0.12 | 3′ SORCS1 |
| Intensive treatment group | |||||||||||||
| 15 | rs493218 | 51,277,554 | 5.2 × 10−7 | 5.4 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | C | T | 0.11 | 2 | 0.20 | 3′ WDR72 |
| 15 | rs572221 | 51,291,924 | 6.6 × 10−7 | 6.8 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 2 | 0.25 | 3′ WDR72 |
| 15 | rs690271 | 51,291,964 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 0 | 0.26 | 3′ WDR72 |
| 15 | rs566369 | 51,295,884 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 1 | 0.26 | 3′ WDR72 |
| 15 | rs482541 | 51,296,486 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 1 | 0.26 | 3′ WDR72 |
| Combined treatment groups | |||||||||||||
| 10 | rs1358030 | 108,113,589 | 3.8 × 10−10 | 2.2 × 10−9 | 7.84 (0.04) | 8.16 (0.04) | 8.36 (0.08) | C | T | 0.36 | 2 | 0.12 | 3′ SORCS1 |
| 14 | rs11624318 | 94,375,765 | 2.7 × 10−7 | 7.6 × 10−6 | 8.07 (0.04) | 8.11 (0.05) | 7.43 (0.12) | A | C | 0.21 | 1 | 0.28 | 5′ GSC |
| 14 | rs11160219 | 94,405,244 | 4.3 × 10−7 | 3.4 × 10−5 | 8.10 (0.04) | 8.08 (0.05) | 7.47 (0.11) | A | G | 0.24 | 1 | 0.49 | 5′ GSC |
| 14 | rs8007115 | 94,407,241 | 5.4 × 10−7 | 4.1 × 10−5 | 8.10 (0.04) | 8.07 (0.05) | 7.47 (0.11) | T | C | 0.23 | 3 | 0.59 | 5′ GSC |
| Chromosome . | SNP . | Position . | Repeated A1C P value . | Mean A1C P value . | Mean A1C by genotype from repeated analysis . | A1 . | A2 . | Minor allele frequency . | Missing data* . | Hardy-Weinberg equilibrium . | Location of SNP to nearest gene . | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C homo (SE) . | Het (SE) . | R homo (SE) . | |||||||||||
| Conventional treatment group | |||||||||||||
| 9 | rs10810632 | 16,779,024 | 9.0 × 10−8 | 3.7 × 10−7 | 8.83 (0.05) | 9.50 (0.13) | 10.50 (0.63) | C | T | 0.08 | 1 | 0.70 | Intron 1 BNC2 |
| 9 | rs6475082 | 16,779,436 | 1.8 × 10−7 | 7.4 × 10−7 | 8.83 (0.05) | 9.48 (0.13) | 10.50 (0.63) | G | A | 0.08 | 1 | 0.71 | Intron 1 BNC2 |
| 9 | rs4961760 | 16,779,878 | 1.6 × 10−7 | 7.1 × 10−7 | 8.83 (0.05) | 9.48 (0.13) | 10.50 (0.63) | C | T | 0.08 | 0 | 0.71 | Intron 1 BNC2 |
| 9 | rs2254193 | 16,791,850 | 2.0 × 10−7 | 1.1 × 10−6 | 8.84 (0.05) | 9.57 (0.15) | 10.47 (0.70) | C | A | 0.07 | 8 | 0.67 | Intron 1 BNC2 |
| 10 | rs1358030 | 108,113,589 | 6.9 × 10−10 | 5.4 × 10−9 | 8.58 (0.07) | 9.12 (0.07) | 9.32 (0.13) | C | T | 0.36 | 2 | 0.12 | 3′ SORCS1 |
| Intensive treatment group | |||||||||||||
| 15 | rs493218 | 51,277,554 | 5.2 × 10−7 | 5.4 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | C | T | 0.11 | 2 | 0.20 | 3′ WDR72 |
| 15 | rs572221 | 51,291,924 | 6.6 × 10−7 | 6.8 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 2 | 0.25 | 3′ WDR72 |
| 15 | rs690271 | 51,291,964 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 0 | 0.26 | 3′ WDR72 |
| 15 | rs566369 | 51,295,884 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 1 | 0.26 | 3′ WDR72 |
| 15 | rs482541 | 51,296,486 | 5.0 × 10−7 | 5.1 × 10−7 | 7.26 (0.04) | 6.99 (0.07) | 6.42 (0.22) | A | G | 0.11 | 1 | 0.26 | 3′ WDR72 |
| Combined treatment groups | |||||||||||||
| 10 | rs1358030 | 108,113,589 | 3.8 × 10−10 | 2.2 × 10−9 | 7.84 (0.04) | 8.16 (0.04) | 8.36 (0.08) | C | T | 0.36 | 2 | 0.12 | 3′ SORCS1 |
| 14 | rs11624318 | 94,375,765 | 2.7 × 10−7 | 7.6 × 10−6 | 8.07 (0.04) | 8.11 (0.05) | 7.43 (0.12) | A | C | 0.21 | 1 | 0.28 | 5′ GSC |
| 14 | rs11160219 | 94,405,244 | 4.3 × 10−7 | 3.4 × 10−5 | 8.10 (0.04) | 8.08 (0.05) | 7.47 (0.11) | A | G | 0.24 | 1 | 0.49 | 5′ GSC |
| 14 | rs8007115 | 94,407,241 | 5.4 × 10−7 | 4.1 × 10−5 | 8.10 (0.04) | 8.07 (0.05) | 7.47 (0.11) | T | C | 0.23 | 3 | 0.59 | 5′ GSC |
Mean A1C values are results from stage 1. Longitudinal repeated A1C P values are the results from stage 2. C homo, Het, and R homo are least square means of A1C in the common homozygote, heterozygote and rare homozygote genotype groups, respectively, with SEs in parentheses, back-transformed from analysis of repeated lnA1C. NB. The statistical results for the repeated A1C were based on normal scores. A1 = minor, A2 = major allele.
*Number of individuals with missing genotype data. Position is the nucleotide location from build 36. Location relative to gene is from dbSNP build 129.